
<!doctype html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module definitions</title>
<style type="text/css"><!--
TT { font-family: lucidatypewriter, lucida console, courier }
--></style></head><body bgcolor="#f0f0f8">

<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
<tr bgcolor="#7799ee">
<td valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong>definitions</strong></big></big> (8 September 2004)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/home/todd/release/pdb2pqr/definitions.py">/home/todd/release/pdb2pqr/definitions.py</a></font></td></tr></table>
    <p><tt>Definitions&nbsp;for&nbsp;PDB2PQR<br>
&nbsp;<br>
This&nbsp;file&nbsp;contains&nbsp;classes&nbsp;associated&nbsp;with&nbsp;Amino&nbsp;Acid&nbsp;and&nbsp;Rotamer<br>
definitions&nbsp;as&nbsp;used&nbsp;by&nbsp;PDB2PQR.<br>
&nbsp;<br>
<a href="#Definition">Definition</a>&nbsp;Files&nbsp;Created&nbsp;by<br>
Jens&nbsp;Erik&nbsp;Nielsen<br>
&nbsp;<br>
Ported&nbsp;to&nbsp;Python&nbsp;by&nbsp;Todd&nbsp;Dolinsky&nbsp;(todd@ccb.wustl.edu)<br>
Washington&nbsp;University&nbsp;in&nbsp;St.&nbsp;Louis</tt></p>

<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#aa55cc">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#fffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
    
<tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;&nbsp;</td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="getopt.html">getopt</a><br>
<a href="math.html">math</a><br>
</td><td width="25%" valign=top><a href="os.html">os</a><br>
<a href="random.html">random</a><br>
</td><td width="25%" valign=top><a href="string.html">string</a><br>
<a href="sys.html">sys</a><br>
</td><td width="25%" valign=top></td></tr></table></td></tr></table>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ee77aa">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
    
<tr><td bgcolor="#ee77aa"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;&nbsp;</td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="structures.html#Atom">structures.Atom</a>(<a href="pdb.html#ATOM">pdb.ATOM</a>)
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="definitions.html#DefinitionAtom">DefinitionAtom</a>
</font></dt></dl>
</dd>
<dt><font face="helvetica, arial"><a href="structures.html#Chain">structures.Chain</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="definitions.html#DefinitionChain">DefinitionChain</a>
</font></dt></dl>
</dd>
<dt><font face="helvetica, arial"><a href="definitions.html#Definition">Definition</a>
</font></dt><dt><font face="helvetica, arial"><a href="structures.html#Residue">structures.Residue</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="definitions.html#DefinitionResidue">DefinitionResidue</a>
</font></dt></dl>
</dd>
</dl>
 
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Definition">class <strong>Definition</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt><a href="#Definition">Definition</a>&nbsp;class<br>
&nbsp;<br>
The&nbsp;<a href="#Definition">Definition</a>&nbsp;class&nbsp;contains&nbsp;the&nbsp;structured&nbsp;definitions&nbsp;found<br>
in&nbsp;the&nbsp;files&nbsp;and&nbsp;several&nbsp;mappings&nbsp;for&nbsp;easy&nbsp;access&nbsp;to&nbsp;the&nbsp;information.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Definition-__init__"><strong>__init__</strong></a>(self)</dt><dd><tt>Create&nbsp;a&nbsp;new&nbsp;<a href="#Definition">Definition</a>&nbsp;Object</tt></dd></dl>

<dl><dt><a name="Definition-getAA"><strong>getAA</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;Amino&nbsp;Acid&nbsp;definition<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;Amino&nbsp;Acid&nbsp;definition&nbsp;in&nbsp;self.<strong>chains</strong>[0]</tt></dd></dl>

<dl><dt><a name="Definition-getNA"><strong>getNA</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;Nucleic&nbsp;Acid&nbsp;definition<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;Nucleic&nbsp;Acid&nbsp;definition&nbsp;-&nbsp;a&nbsp;list&nbsp;of&nbsp;Nucleic&nbsp;Acid<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;residues</tt></dd></dl>

<dl><dt><a name="Definition-parseDefinition"><strong>parseDefinition</strong></a>(self, reslines, name, restype)</dt><dd><tt>Parse&nbsp;the&nbsp;definition&nbsp;file,&nbsp;obtaining&nbsp;information&nbsp;about&nbsp;each&nbsp;atom,<br>
its&nbsp;position,&nbsp;and&nbsp;its&nbsp;bonding&nbsp;information.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;reslines:&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;lines&nbsp;containing&nbsp;each&nbsp;of&nbsp;the&nbsp;atoms&nbsp;of&nbsp;the<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;residue&nbsp;(list)<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;restype:&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;of&nbsp;the&nbsp;residue&nbsp;(int)<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;myResidue:&nbsp;The&nbsp;parsed&nbsp;residue&nbsp;(<a href="#DefinitionResidue">DefinitionResidue</a>)</tt></dd></dl>

<dl><dt><a name="Definition-parseRotamer"><strong>parseRotamer</strong></a>(self, reslines)</dt><dd><tt>Parse&nbsp;ROTAMER.DAT,&nbsp;obtaining&nbsp;information&nbsp;about&nbsp;each&nbsp;atom&nbsp;and&nbsp;its<br>
position.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;reslines:&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;lines&nbsp;containing&nbsp;each&nbsp;of&nbsp;the&nbsp;atoms&nbsp;of&nbsp;the<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;residue&nbsp;(list)<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;myResidue:&nbsp;The&nbsp;parsed&nbsp;residue&nbsp;(<a href="#DefinitionResidue">DefinitionResidue</a>)</tt></dd></dl>

<dl><dt><a name="Definition-readDefinition"><strong>readDefinition</strong></a>(self, defpath)</dt><dd><tt>Read&nbsp;a&nbsp;definition&nbsp;file<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;deffile:&nbsp;The&nbsp;path&nbsp;to&nbsp;the&nbsp;definition&nbsp;file&nbsp;(string)<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;def:&nbsp;&nbsp;The&nbsp;definition&nbsp;chain&nbsp;(AADefinition)</tt></dd></dl>

<dl><dt><a name="Definition-readRotamerDefinition"><strong>readRotamerDefinition</strong></a>(self)</dt><dd><tt>Read&nbsp;the&nbsp;Rotamer&nbsp;definitions</tt></dd></dl>

<hr>
Data and non-method functions defined here:<br>
<dl><dt><strong>__doc__</strong> = '<font color="#c040c0">\n</font>        Definition class<font color="#c040c0">\n\n</font>        The Definitio...mappings for easy access to the information.<font color="#c040c0">\n</font>    '</dl>

<dl><dt><strong>__module__</strong> = 'definitions'</dl>

</td></tr></table> 
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="DefinitionAtom">class <strong>DefinitionAtom</strong></a>(<a href="structures.html#Atom">structures.Atom</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Class&nbsp;<a href="#DefinitionAtom">DefinitionAtom</a><br>
&nbsp;<br>
The&nbsp;<a href="#DefinitionAtom">DefinitionAtom</a>&nbsp;class&nbsp;inherits&nbsp;off&nbsp;the&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;class.&nbsp;&nbsp;It&nbsp;provides<br>
a&nbsp;trimmed&nbsp;down&nbsp;version&nbsp;of&nbsp;the&nbsp;initializating&nbsp;function&nbsp;from&nbsp;the&nbsp;<a href="structures.html#Atom">Atom</a><br>
class&nbsp;for&nbsp;the&nbsp;definition&nbsp;files.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="definitions.html#DefinitionAtom">DefinitionAtom</a></dd>
<dd><a href="structures.html#Atom">structures.Atom</a></dd>
<dd><a href="pdb.html#ATOM">pdb.ATOM</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="DefinitionAtom-__init__"><strong>__init__</strong></a>(self, serial, name, resName, x, y, z)</dt><dd><tt>Initialize&nbsp;using&nbsp;a&nbsp;few&nbsp;basic&nbsp;parameters&nbsp;-&nbsp;set&nbsp;all&nbsp;other&nbsp;fields<br>
to&nbsp;null,&nbsp;which&nbsp;is&nbsp;necessary&nbsp;for&nbsp;debugging&nbsp;output&nbsp;by&nbsp;using&nbsp;the<br>
string&nbsp;function&nbsp;in&nbsp;the&nbsp;parent&nbsp;class.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;serial:&nbsp;&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;serial&nbsp;number&nbsp;(int)<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;name.&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;resName:&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;name.&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;sequence&nbsp;number.&nbsp;(int)<br>
&nbsp;&nbsp;&nbsp;&nbsp;x:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;X&nbsp;in&nbsp;Angstroms.&nbsp;(float)<br>
&nbsp;&nbsp;&nbsp;&nbsp;y:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Y&nbsp;in&nbsp;Angstroms.&nbsp;(float)<br>
&nbsp;&nbsp;&nbsp;&nbsp;z:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Z&nbsp;in&nbsp;Angstroms.&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="DefinitionAtom-isBackbone"><strong>isBackbone</strong></a>(self)</dt><dd><tt>Return&nbsp;true&nbsp;if&nbsp;atom&nbsp;name&nbsp;is&nbsp;in&nbsp;backbone,&nbsp;otherwise&nbsp;false<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;state:&nbsp;1&nbsp;if&nbsp;true,&nbsp;0&nbsp;if&nbsp;false</tt></dd></dl>

<hr>
Data and non-method functions defined here:<br>
<dl><dt><strong>__doc__</strong> = '<font color="#c040c0">\n</font>        Class DefinitionAtom<font color="#c040c0">\n\n</font>        The Defin...Atom<font color="#c040c0">\n</font>        class for the definition files.<font color="#c040c0">\n</font>    '</dl>

<dl><dt><strong>__module__</strong> = 'definitions'</dl>

<hr>
Methods inherited from <a href="structures.html#Atom">structures.Atom</a>:<br>
<dl><dt><a name="DefinitionAtom-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Returns&nbsp;a&nbsp;string&nbsp;of&nbsp;the&nbsp;new&nbsp;atom&nbsp;type.&nbsp;&nbsp;Uses&nbsp;the&nbsp;ATOM&nbsp;string<br>
output&nbsp;but&nbsp;changes&nbsp;the&nbsp;first&nbsp;field&nbsp;to&nbsp;either&nbsp;by&nbsp;ATOM&nbsp;or<br>
HETATM&nbsp;as&nbsp;necessary.<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;out:&nbsp;String&nbsp;with&nbsp;ATOM/HETATM&nbsp;field&nbsp;set&nbsp;appropriately</tt></dd></dl>

<dl><dt><a name="DefinitionAtom-addExtraBond"><strong>addExtraBond</strong></a>(self, bondedatom)</dt><dd><tt>Add&nbsp;a&nbsp;bond&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;extrabonds<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;bondedatom:&nbsp;The&nbsp;atom&nbsp;to&nbsp;bond&nbsp;to&nbsp;(<a href="structures.html#Atom">Atom</a>)</tt></dd></dl>

<dl><dt><a name="DefinitionAtom-addIntraBond"><strong>addIntraBond</strong></a>(self, bondedatom)</dt><dd><tt>Add&nbsp;a&nbsp;bond&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;intrabonds<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;bondedatom:&nbsp;The&nbsp;atom&nbsp;to&nbsp;bond&nbsp;to&nbsp;(<a href="structures.html#Atom">Atom</a>)</tt></dd></dl>

<dl><dt><a name="DefinitionAtom-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;of&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;(either&nbsp;ATOM&nbsp;or&nbsp;HETATM)<br>
&nbsp;&nbsp;&nbsp;&nbsp;serial:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;serial&nbsp;number<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;name<br>
&nbsp;&nbsp;&nbsp;&nbsp;altLoc:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Alternate&nbsp;location<br>
&nbsp;&nbsp;&nbsp;&nbsp;resName:&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;name<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Chain">Chain</a>&nbsp;identifier<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;sequence&nbsp;number<br>
&nbsp;&nbsp;&nbsp;&nbsp;iCode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Code&nbsp;for&nbsp;insertion&nbsp;of&nbsp;residues<br>
&nbsp;&nbsp;&nbsp;&nbsp;x:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;X&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;y:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Y&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;z:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Z&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;occupancy:&nbsp;&nbsp;Occupancy<br>
&nbsp;&nbsp;&nbsp;&nbsp;tempFactor:&nbsp;Temperature&nbsp;Factor<br>
&nbsp;&nbsp;&nbsp;&nbsp;segID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Segment&nbsp;identifier<br>
&nbsp;&nbsp;&nbsp;&nbsp;element:&nbsp;&nbsp;&nbsp;&nbsp;Element&nbsp;symbol<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Charge&nbsp;on&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;bonds:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;bonds&nbsp;associated&nbsp;with&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;interbonds:&nbsp;The&nbsp;intrabonds&nbsp;associated&nbsp;with&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;extrabonds:&nbsp;The&nbsp;extrabonds&nbsp;assocaited&nbsp;with&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;residue:&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;parent&nbsp;residue&nbsp;of&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;radius:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;radius&nbsp;of&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;ffcharge:&nbsp;&nbsp;&nbsp;The&nbsp;forcefield&nbsp;charge&nbsp;on&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;hdonor:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Whether&nbsp;the&nbsp;atom&nbsp;is&nbsp;a&nbsp;hydrogen&nbsp;donor<br>
&nbsp;&nbsp;&nbsp;&nbsp;hacceptor:&nbsp;&nbsp;Whether&nbsp;the&nbsp;atom&nbsp;is&nbsp;a&nbsp;hydrogen&nbsp;acceptor<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="DefinitionAtom-getCoords"><strong>getCoords</strong></a>(self)</dt><dd><tt>Return&nbsp;the&nbsp;x,y,z&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;in&nbsp;list&nbsp;form<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;the&nbsp;coordinates&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="DefinitionAtom-isHydrogen"><strong>isHydrogen</strong></a>(self)</dt><dd><tt>Is&nbsp;this&nbsp;atom&nbsp;a&nbsp;Hydrogen&nbsp;atom?<br>
&nbsp;<br>
returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;1&nbsp;if&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;is&nbsp;a&nbsp;Hydrogen,&nbsp;0&nbsp;otherwise</tt></dd></dl>

<dl><dt><a name="DefinitionAtom-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;to&nbsp;set&nbsp;the&nbsp;member&nbsp;to<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;of&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;(either&nbsp;ATOM&nbsp;or&nbsp;HETATM)<br>
&nbsp;&nbsp;&nbsp;&nbsp;serial:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;serial&nbsp;number<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;name<br>
&nbsp;&nbsp;&nbsp;&nbsp;altLoc:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Alternate&nbsp;location<br>
&nbsp;&nbsp;&nbsp;&nbsp;resName:&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;name<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Chain">Chain</a>&nbsp;identifier<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;sequence&nbsp;number<br>
&nbsp;&nbsp;&nbsp;&nbsp;iCode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Code&nbsp;for&nbsp;insertion&nbsp;of&nbsp;residues<br>
&nbsp;&nbsp;&nbsp;&nbsp;x:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;X&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;y:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Y&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;z:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Z&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;occupancy:&nbsp;&nbsp;Occupancy<br>
&nbsp;&nbsp;&nbsp;&nbsp;tempFactor:&nbsp;Temperature&nbsp;Factor<br>
&nbsp;&nbsp;&nbsp;&nbsp;segID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Segment&nbsp;identifier<br>
&nbsp;&nbsp;&nbsp;&nbsp;element:&nbsp;&nbsp;&nbsp;&nbsp;Element&nbsp;symbol<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Charge&nbsp;on&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;residue:&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;parent&nbsp;residue&nbsp;of&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;radius:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;radius&nbsp;of&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;ffcharge:&nbsp;&nbsp;&nbsp;The&nbsp;forcefield&nbsp;charge&nbsp;on&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;hdonor:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Whether&nbsp;the&nbsp;atom&nbsp;is&nbsp;a&nbsp;hydrogen&nbsp;donor<br>
&nbsp;&nbsp;&nbsp;&nbsp;hacceptor:&nbsp;&nbsp;Whether&nbsp;the&nbsp;atom&nbsp;is&nbsp;a&nbsp;hydrogen&nbsp;acceptor<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

</td></tr></table> 
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="DefinitionChain">class <strong>DefinitionChain</strong></a>(<a href="structures.html#Chain">structures.Chain</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt><a href="#DefinitionChain">DefinitionChain</a>&nbsp;class<br>
&nbsp;<br>
The&nbsp;<a href="#DefinitionChain">DefinitionChain</a>&nbsp;class&nbsp;extends&nbsp;the&nbsp;chain&nbsp;class&nbsp;to&nbsp;provide<br>
lookups&nbsp;for&nbsp;atom&nbsp;information.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="DefinitionChain-__init__"><strong>__init__</strong></a>(self, ID)</dt><dd><tt>Initialize&nbsp;like&nbsp;the&nbsp;<a href="structures.html#Chain">Chain</a>&nbsp;constructor,&nbsp;but&nbsp;add&nbsp;necessary<br>
features<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;ID:&nbsp;The&nbsp;ID&nbsp;of&nbsp;the&nbsp;chain</tt></dd></dl>

<dl><dt><a name="DefinitionChain-addResidue"><strong>addResidue</strong></a>(self, residue)</dt><dd><tt>Add&nbsp;a&nbsp;residue&nbsp;to&nbsp;the&nbsp;chain<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;residue:&nbsp;The&nbsp;residue&nbsp;to&nbsp;be&nbsp;added&nbsp;(<a href="structures.html#Residue">Residue</a>)</tt></dd></dl>

<dl><dt><a name="DefinitionChain-getResidue"><strong>getResidue</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;a&nbsp;residue&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<hr>
Data and non-method functions defined here:<br>
<dl><dt><strong>__doc__</strong> = '<font color="#c040c0">\n</font>        DefinitionChain class<font color="#c040c0">\n\n</font>        The Defi...rovide<font color="#c040c0">\n</font>        lookups for atom information.<font color="#c040c0">\n</font>    '</dl>

<dl><dt><strong>__module__</strong> = 'definitions'</dl>

<hr>
Methods inherited from <a href="structures.html#Chain">structures.Chain</a>:<br>
<dl><dt><a name="DefinitionChain-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="structures.html#Chain">Chain</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;ID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;ID&nbsp;of&nbsp;the&nbsp;chain<br>
&nbsp;&nbsp;&nbsp;&nbsp;Residues:&nbsp;The&nbsp;list&nbsp;of&nbsp;residues&nbsp;within&nbsp;the&nbsp;<a href="structures.html#Chain">Chain</a><br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="DefinitionChain-getAtoms"><strong>getAtoms</strong></a>(self)</dt><dd><tt>Return&nbsp;a&nbsp;list&nbsp;of&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;objects&nbsp;contained&nbsp;in&nbsp;this&nbsp;chain<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomlist:&nbsp;List&nbsp;of&nbsp;<a href="structures.html#Atom">Atom</a>&nbsp;objects&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="DefinitionChain-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;chain<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;chain&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="DefinitionChain-numResidues"><strong>numResidues</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;residues&nbsp;for&nbsp;the&nbsp;chain<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;residues&nbsp;in&nbsp;the&nbsp;chain&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="DefinitionChain-renumberResidues"><strong>renumberResidues</strong></a>(self)</dt><dd><tt>Renumber&nbsp;Atoms&nbsp;based&nbsp;on&nbsp;actual&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;number&nbsp;and&nbsp;not&nbsp;PDB&nbsp;resSeq</tt></dd></dl>

</td></tr></table> 
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="DefinitionResidue">class <strong>DefinitionResidue</strong></a>(<a href="structures.html#Residue">structures.Residue</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt><a href="#DefinitionResidue">DefinitionResidue</a>&nbsp;class<br>
&nbsp;<br>
The&nbsp;<a href="#DefinitionResidue">DefinitionResidue</a>&nbsp;class&nbsp;extends&nbsp;the&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;allow&nbsp;for&nbsp;a<br>
trimmed&nbsp;down&nbsp;initializing&nbsp;function.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="DefinitionResidue-__init__"><strong>__init__</strong></a>(self, name, type)</dt><dd><tt>Initialize&nbsp;the&nbsp;class&nbsp;using&nbsp;a&nbsp;few&nbsp;parameters<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;The&nbsp;abbreviated&nbsp;amino&nbsp;acid&nbsp;name&nbsp;of&nbsp;the&nbsp;<a href="#DefinitionResidue">DefinitionResidue</a><br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;The&nbsp;typecode&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Available&nbsp;typecodes&nbsp;are:<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1:&nbsp;Protein&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2:&nbsp;Drug/small-molecule<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3:&nbsp;Water<br>
&nbsp;&nbsp;&nbsp;&nbsp;number:&nbsp;ID&nbsp;number&nbsp;for&nbsp;residue</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-addDihedral"><strong>addDihedral</strong></a>(self, atom)</dt><dd><tt>Add&nbsp;the&nbsp;atom&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;dihedral&nbsp;bonds<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom:&nbsp;The&nbsp;atom&nbsp;to&nbsp;be&nbsp;added</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-makeBondList"><strong>makeBondList</strong></a>(self, residue, atomname)</dt><dd><tt>For&nbsp;the&nbsp;given&nbsp;atomname,&nbsp;make&nbsp;a&nbsp;list&nbsp;of&nbsp;bonded&nbsp;atoms.<br>
First&nbsp;get&nbsp;all&nbsp;atoms&nbsp;present&nbsp;in&nbsp;the&nbsp;residue&nbsp;that&nbsp;are<br>
directly&nbsp;bonded&nbsp;to&nbsp;the&nbsp;atom&nbsp;-&nbsp;if&nbsp;this&nbsp;number&nbsp;is<br>
less&nbsp;than&nbsp;REFATOM_SIZE,&nbsp;take&nbsp;those&nbsp;atoms&nbsp;that&nbsp;are&nbsp;present&nbsp;and<br>
bonded&nbsp;to&nbsp;initial&nbsp;bond&nbsp;list&nbsp;and&nbsp;use&nbsp;them.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;residue:&nbsp;&nbsp;The&nbsp;residue&nbsp;to&nbsp;check&nbsp;for&nbsp;present&nbsp;atoms&nbsp;(<a href="structures.html#Residue">Residue</a>)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;atom&nbsp;name&nbsp;to&nbsp;sedd&nbsp;the&nbsp;list&nbsp;of&nbsp;bonds&nbsp;(string)<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;bonds:&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;atomnames&nbsp;that&nbsp;are&nbsp;within&nbsp;two&nbsp;bonds&nbsp;of<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;atom&nbsp;and&nbsp;present&nbsp;in&nbsp;residue&nbsp;(list)</tt></dd></dl>

<hr>
Data and non-method functions defined here:<br>
<dl><dt><strong>__doc__</strong> = '<font color="#c040c0">\n</font>        DefinitionResidue class<font color="#c040c0">\n\n</font>        The De...<font color="#c040c0">\n</font>        trimmed down initializing function.<font color="#c040c0">\n</font>    '</dl>

<dl><dt><strong>__module__</strong> = 'definitions'</dl>

<hr>
Methods inherited from <a href="structures.html#Residue">structures.Residue</a>:<br>
<dl><dt><a name="DefinitionResidue-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Add&nbsp;the&nbsp;atom&nbsp;object&nbsp;to&nbsp;the&nbsp;residue.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom:&nbsp;The&nbsp;object&nbsp;to&nbsp;be&nbsp;added&nbsp;(ATOM)</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-addChiangle"><strong>addChiangle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-addDebumpAtom"><strong>addDebumpAtom</strong></a>(self, atom)</dt><dd><tt>Add&nbsp;an&nbsp;atom&nbsp;to&nbsp;the&nbsp;check&nbsp;for&nbsp;debumping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom:&nbsp;&nbsp;The&nbsp;atom&nbsp;to&nbsp;add&nbsp;to&nbsp;the&nbsp;list</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-checkAtomNames"><strong>checkAtomNames</strong></a>(self)</dt><dd><tt>Check&nbsp;to&nbsp;see&nbsp;if&nbsp;there&nbsp;are&nbsp;any&nbsp;misnamed&nbsp;hydrogens&nbsp;within&nbsp;the<br>
residue.&nbsp;&nbsp;Converts&nbsp;hydrogens&nbsp;of&nbsp;type&nbsp;1HH1&nbsp;and&nbsp;2H*&nbsp;to&nbsp;HH11&nbsp;and<br>
H*2&nbsp;to&nbsp;easily&nbsp;compare&nbsp;with&nbsp;the&nbsp;Amino&nbsp;Acid&nbsp;definition&nbsp;file.&nbsp;Also<br>
converts&nbsp;H*1&nbsp;and&nbsp;H*2&nbsp;to&nbsp;H*2&nbsp;and&nbsp;H*3&nbsp;when&nbsp;necessary.&nbsp;Rename&nbsp;the<br>
atom&nbsp;and&nbsp;update&nbsp;the&nbsp;residue.</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-createAtom"><strong>createAtom</strong></a>(self, name, newcoords, type)</dt><dd><tt>Add&nbsp;a&nbsp;new&nbsp;atom&nbsp;object&nbsp;to&nbsp;the&nbsp;residue.&nbsp;Uses&nbsp;an&nbsp;atom<br>
currently&nbsp;in&nbsp;the&nbsp;residue&nbsp;to&nbsp;seed&nbsp;the&nbsp;new&nbsp;atom<br>
object,&nbsp;then&nbsp;replaces&nbsp;the&nbsp;coordinates&nbsp;and&nbsp;name&nbsp;accordingly.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;new&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;x,y,z&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;new&nbsp;atom&nbsp;(list)<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;of&nbsp;atom,&nbsp;ATOM&nbsp;or&nbsp;HETATM</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="DefinitionResidue-updateIntraBonds"><strong>updateIntraBonds</strong></a>(self, defresidue)</dt><dd><tt>Update&nbsp;the&nbsp;IntraBonds&nbsp;for&nbsp;each&nbsp;atom&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;defresidue:&nbsp;&nbsp;The&nbsp;definition&nbsp;residue&nbsp;(<a href="#DefinitionResidue">DefinitionResidue</a>)</tt></dd></dl>

</td></tr></table></td></tr></table>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#eeaa77">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
    
<tr><td bgcolor="#eeaa77"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;&nbsp;</td>
<td width="100%"><dl><dt><a name="-acos"><strong>acos</strong></a>(...)</dt><dd><tt><a href="#-acos">acos</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;arc&nbsp;cosine&nbsp;(measured&nbsp;in&nbsp;radians)&nbsp;of&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-asin"><strong>asin</strong></a>(...)</dt><dd><tt><a href="#-asin">asin</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;arc&nbsp;sine&nbsp;(measured&nbsp;in&nbsp;radians)&nbsp;of&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-atan"><strong>atan</strong></a>(...)</dt><dd><tt><a href="#-atan">atan</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;arc&nbsp;tangent&nbsp;(measured&nbsp;in&nbsp;radians)&nbsp;of&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-atan2"><strong>atan2</strong></a>(...)</dt><dd><tt><a href="#-atan2">atan2</a>(y,&nbsp;x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;arc&nbsp;tangent&nbsp;(measured&nbsp;in&nbsp;radians)&nbsp;of&nbsp;y/x.<br>
Unlike&nbsp;<a href="#-atan">atan</a>(y/x),&nbsp;the&nbsp;signs&nbsp;of&nbsp;both&nbsp;x&nbsp;and&nbsp;y&nbsp;are&nbsp;considered.</tt></dd></dl>
 <dl><dt><a name="-ceil"><strong>ceil</strong></a>(...)</dt><dd><tt><a href="#-ceil">ceil</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;ceiling&nbsp;of&nbsp;x&nbsp;as&nbsp;a&nbsp;float.<br>
This&nbsp;is&nbsp;the&nbsp;smallest&nbsp;integral&nbsp;value&nbsp;&gt;=&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-cos"><strong>cos</strong></a>(...)</dt><dd><tt><a href="#-cos">cos</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;cosine&nbsp;of&nbsp;x&nbsp;(measured&nbsp;in&nbsp;radians).</tt></dd></dl>
 <dl><dt><a name="-cosh"><strong>cosh</strong></a>(...)</dt><dd><tt><a href="#-cosh">cosh</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;hyperbolic&nbsp;cosine&nbsp;of&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-exp"><strong>exp</strong></a>(...)</dt><dd><tt><a href="#-exp">exp</a>(x)<br>
&nbsp;<br>
Return&nbsp;e&nbsp;raised&nbsp;to&nbsp;the&nbsp;power&nbsp;of&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-fabs"><strong>fabs</strong></a>(...)</dt><dd><tt><a href="#-fabs">fabs</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;absolute&nbsp;value&nbsp;of&nbsp;the&nbsp;float&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-floor"><strong>floor</strong></a>(...)</dt><dd><tt><a href="#-floor">floor</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;floor&nbsp;of&nbsp;x&nbsp;as&nbsp;a&nbsp;float.<br>
This&nbsp;is&nbsp;the&nbsp;largest&nbsp;integral&nbsp;value&nbsp;&lt;=&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-fmod"><strong>fmod</strong></a>(...)</dt><dd><tt><a href="#-fmod">fmod</a>(x,y)<br>
&nbsp;<br>
Return&nbsp;<a href="#-fmod">fmod</a>(x,&nbsp;y),&nbsp;according&nbsp;to&nbsp;platform&nbsp;C.&nbsp;&nbsp;x&nbsp;%&nbsp;y&nbsp;may&nbsp;differ.</tt></dd></dl>
 <dl><dt><a name="-frexp"><strong>frexp</strong></a>(...)</dt><dd><tt><a href="#-frexp">frexp</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;mantissa&nbsp;and&nbsp;exponent&nbsp;of&nbsp;x,&nbsp;as&nbsp;pair&nbsp;(m,&nbsp;e).<br>
m&nbsp;is&nbsp;a&nbsp;float&nbsp;and&nbsp;e&nbsp;is&nbsp;an&nbsp;int,&nbsp;such&nbsp;that&nbsp;x&nbsp;=&nbsp;m&nbsp;*&nbsp;2.**e.<br>
If&nbsp;x&nbsp;is&nbsp;0,&nbsp;m&nbsp;and&nbsp;e&nbsp;are&nbsp;both&nbsp;0.&nbsp;&nbsp;Else&nbsp;0.5&nbsp;&lt;=&nbsp;abs(m)&nbsp;&lt;&nbsp;1.0.</tt></dd></dl>
 <dl><dt><a name="-hypot"><strong>hypot</strong></a>(...)</dt><dd><tt><a href="#-hypot">hypot</a>(x,y)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;Euclidean&nbsp;distance,&nbsp;<a href="#-sqrt">sqrt</a>(x*x&nbsp;+&nbsp;y*y).</tt></dd></dl>
 <dl><dt><a name="-ldexp"><strong>ldexp</strong></a>(...)</dt><dd><tt><a href="#-ldexp">ldexp</a>(x,&nbsp;i)&nbsp;-&gt;&nbsp;x&nbsp;*&nbsp;(2**i)</tt></dd></dl>
 <dl><dt><a name="-log"><strong>log</strong></a>(...)</dt><dd><tt><a href="#-log">log</a>(x)&nbsp;-&gt;&nbsp;the&nbsp;natural&nbsp;logarithm&nbsp;(base&nbsp;e)&nbsp;of&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-log10"><strong>log10</strong></a>(...)</dt><dd><tt><a href="#-log10">log10</a>(x)&nbsp;-&gt;&nbsp;the&nbsp;base&nbsp;10&nbsp;logarithm&nbsp;of&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-modf"><strong>modf</strong></a>(...)</dt><dd><tt><a href="#-modf">modf</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;fractional&nbsp;and&nbsp;integer&nbsp;parts&nbsp;of&nbsp;x.&nbsp;&nbsp;Both&nbsp;results&nbsp;carry&nbsp;the&nbsp;sign<br>
of&nbsp;x.&nbsp;&nbsp;The&nbsp;integer&nbsp;part&nbsp;is&nbsp;returned&nbsp;as&nbsp;a&nbsp;real.</tt></dd></dl>
 <dl><dt><a name="-pow"><strong>pow</strong></a>(...)</dt><dd><tt><a href="#-pow">pow</a>(x,y)<br>
&nbsp;<br>
Return&nbsp;x**y&nbsp;(x&nbsp;to&nbsp;the&nbsp;power&nbsp;of&nbsp;y).</tt></dd></dl>
 <dl><dt><a name="-sin"><strong>sin</strong></a>(...)</dt><dd><tt><a href="#-sin">sin</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;sine&nbsp;of&nbsp;x&nbsp;(measured&nbsp;in&nbsp;radians).</tt></dd></dl>
 <dl><dt><a name="-sinh"><strong>sinh</strong></a>(...)</dt><dd><tt><a href="#-sinh">sinh</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;hyperbolic&nbsp;sine&nbsp;of&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-sqrt"><strong>sqrt</strong></a>(...)</dt><dd><tt><a href="#-sqrt">sqrt</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;square&nbsp;root&nbsp;of&nbsp;x.</tt></dd></dl>
 <dl><dt><a name="-tan"><strong>tan</strong></a>(...)</dt><dd><tt><a href="#-tan">tan</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;tangent&nbsp;of&nbsp;x&nbsp;(measured&nbsp;in&nbsp;radians).</tt></dd></dl>
 <dl><dt><a name="-tanh"><strong>tanh</strong></a>(...)</dt><dd><tt><a href="#-tanh">tanh</a>(x)<br>
&nbsp;<br>
Return&nbsp;the&nbsp;hyperbolic&nbsp;tangent&nbsp;of&nbsp;x.</tt></dd></dl>
</td></tr></table>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#55aa55">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
    
<tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;&nbsp;</td>
<td width="100%"><strong>AAFILE</strong> = 'AA.DAT'<br>
<strong>AAS</strong> = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLH', 'GLY', 'HIS', 'HID', 'HIE', 'HIP', 'HSD', 'HSE', 'HSP', 'ILE', 'LEU', 'LYS', 'MET', ...]<br>
<strong>AMBER_FILE</strong> = 'AMBER.DAT'<br>
<strong>BACKBONE</strong> = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN']<br>
<strong>BONDED_SS_LIMIT</strong> = 2.5<br>
<strong>BUMP_DIST</strong> = 2.0<br>
<strong>BUMP_HDIST</strong> = 1.5<br>
<strong>CELL_SIZE</strong> = 2<br>
<strong>CHARMM_FILE</strong> = 'CHARMM.DAT'<br>
<strong>DIHEDRAL</strong> = 57.2958<br>
<strong>HYDRO_BONDCOORDS</strong> = [[7.5810000000000004, 2.0899999999999999, 12.506], [6.4580000000000002, 2.1619999999999999, 13.159000000000001], [5.1449999999999996, 2.2090000000000001, 12.452999999999999]]<br>
<strong>HYDRO_COORDS</strong> = [6.476, 2.1859999999999999, 14.159000000000001]<br>
<strong>LARGE_TORSION_ANGLE</strong> = 1000.0<br>
<strong>NAFILE</strong> = 'NA.DAT'<br>
<strong>NAS</strong> = ['A', 'A5', 'A3', 'C', 'C5', 'C3', 'G', 'G5', 'G3', 'T', 'T5', 'T3', 'U', 'U5', 'U3']<br>
<strong>NTERM2_COORDS</strong> = [-24.001000000000001, 50.223999999999997, -22.225999999999999]<br>
<strong>NTERM3_COORDS</strong> = [-24.869, 48.845999999999997, -22.77]<br>
<strong>NTERM_COORDS</strong> = [[-24.196000000000002, 48.789999999999999, -20.800000000000001], [-25.552, 49.881, -21.847999999999999], [-24.645, 49.491, -22.007000000000001]]<br>
<strong>OXT_COORDS</strong> = [-1.5289999999999999, 1.8580000000000001, 0.69499999999999995]<br>
<strong>PARSE_FILE</strong> = 'PARSE.DAT'<br>
<strong>PEPTIDE_DIST</strong> = 1.7<br>
<strong>PEP_TRANS_CA</strong> = [-2.3130000000000002, 2.7839999999999998, 1.0229999999999999]<br>
<strong>PEP_TRANS_N</strong> = [-1.252, 1.877, 0.88300000000000001]<br>
<strong>REFATOM_SIZE</strong> = 3<br>
<strong>REPAIR_LIMIT</strong> = 10<br>
<strong>ROTAMERFILE</strong> = 'ROTAMER.DAT'<br>
<strong>SMALL</strong> = 9.9999999999999995e-08<br>
<strong>__author__</strong> = 'Jens Erik Nielsen, Todd Dolinsky'<br>
<strong>__date__</strong> = '8 September 2004'<br>
<strong>__file__</strong> = './definitions.pyc'<br>
<strong>__name__</strong> = 'definitions'<br>
<strong>e</strong> = 2.7182818284590451<br>
<strong>pi</strong> = 3.1415926535897931</td></tr></table>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
    
<tr><td bgcolor="#7799ee"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;&nbsp;</td>
<td width="100%">Jens&nbsp;Erik&nbsp;Nielsen,&nbsp;Todd&nbsp;Dolinsky</td></tr></table>
</body></html>